iMeta最新文献

{"title":"Isolation of potentially novel species expands the genomic and functional diversity of Lachnospiraceae","authors":"Xiaoqian Lin,&nbsp;Tongyuan Hu,&nbsp;Zhinan Wu,&nbsp;Lingne Li,&nbsp;Yuhao Wang,&nbsp;Dingyang Wen,&nbsp;Xudong Liu,&nbsp;Wenxi Li,&nbsp;Hewei Liang,&nbsp;Xin Jin,&nbsp;Xun Xu,&nbsp;Jian Wang,&nbsp;Huanming Yang,&nbsp;Karsten Kristiansen,&nbsp;Liang Xiao,&nbsp;Yuanqiang Zou","doi":"10.1002/imt2.174","DOIUrl":"10.1002/imt2.174","url":null,"abstract":"<p>The Lachnospiraceae family holds promise as a source of next-generation probiotics, yet a comprehensive delineation of its diversity is lacking, hampering the identification of suitable strains for future applications. To address this knowledge gap, we conducted an in-depth genomic and functional analysis of 1868 high-quality genomes, combining data from public databases with our new isolates. This data set represented 387 colonization-selective species-level clusters, of which eight genera represented multilineage clusters. Pan-genome analysis, single-nucleotide polymorphism (SNP) identification, and probiotic functional predictions revealed that species taxonomy, habitats, and geography together shape the functional diversity of Lachnospiraceae. Moreover, analyses of associations with atherosclerotic cardiovascular disease (ACVD) and inflammatory bowel disease (IBD) indicated that several strains of potentially novel Lachnospiraceae species possess the capacity to reduce the abundance of opportunistic pathogens, thereby imparting potential health benefits. Our findings shed light on the untapped potential of novel species enabling knowledge-based selection of strains for the development of next-generation probiotics holding promise for improving human health and disease management.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.174","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139840546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacterial load in meconium","authors":"Wen-Yu Jin,&nbsp;Jing Peng,&nbsp;Jinping Dai,&nbsp;Rongkang Tang,&nbsp;Jia-Xin Guo,&nbsp;Huan Zhao,&nbsp;Jielin Wang,&nbsp;Shu Zhang,&nbsp;Yi-Zhou Gao","doi":"10.1002/imt2.173","DOIUrl":"10.1002/imt2.173","url":null,"abstract":"<p>The spike-in plasmid method was utilized to perform an analysis on meconium and second-pass feces, yielding both relative and absolute quantitative results. With the absolute quantitative data, the abundance of bacteria in 17 meconium samples and 17 second-pass fecal samples were found to be 1.14 × 10⁷ and 1.59 × 10⁹ copies/g, respectively. The mode of delivery can significantly influence the alterations and compositions of gut bacteria in a newborn within 72 h.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.173","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139779578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Wekemo Bioincloud: A user-friendly platform for meta-omics data analyses","authors":"Yunyun Gao,&nbsp;Guoxing Zhang,&nbsp;Shunyao Jiang,&nbsp;Yong-Xin Liu","doi":"10.1002/imt2.175","DOIUrl":"10.1002/imt2.175","url":null,"abstract":"<p>The increasing application of meta-omics approaches to investigate the structure, function, and intercellular interactions of microbial communities has led to a surge in available data. However, this abundance of human and environmental microbiome data has exposed new scalability challenges for existing bioinformatics tools. In response, we introduce Wekemo Bioincloud—a specialized platform for -omics studies. This platform offers a comprehensive analysis solution, specifically designed to alleviate the challenges of tool selection for users in the face of expanding data sets. As of now, Wekemo Bioincloud has been regularly equipped with 22 workflows and 65 visualization tools, establishing itself as a user-friendly and widely embraced platform for studying diverse data sets. Additionally, the platform enables the online modification of vector outputs, and the registration-independent personalized dashboard system ensures privacy and traceability. Wekemo Bioincloud is freely available at https://www.bioincloud.tech/.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.175","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139840332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthetic microbial communities: Sandbox and blueprint for soil health enhancement","authors":"Mei Li,&nbsp;Jie Hu,&nbsp;Zhong Wei,&nbsp;Alexandre Jousset,&nbsp;Thomas Pommier,&nbsp;Xiangyang Yu,&nbsp;Yangchun Xu,&nbsp;Qirong Shen","doi":"10.1002/imt2.172","DOIUrl":"https://doi.org/10.1002/imt2.172","url":null,"abstract":"<p>We summarize here the use of SynComs in improving various dimensions of soil health, including fertility, pollutant removal, soil-borne disease suppression, and soil resilience; as well as a set of useful guidelines to assess and understand the principles for designing SynComs to enhance soil health. Finally, we discuss the next stages of SynComs applications, including highly diverse and multikingdom SynComs targeting several functions simultaneously.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.172","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139915591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A comprehensive analysis of antibiotic resistance genes in the giant panda gut","authors":"Feilong Deng,&nbsp;Yanhua Han,&nbsp;Yushan Huang,&nbsp;Desheng Li,&nbsp;Jianmin Chai,&nbsp;Linhua Deng,&nbsp;Ming Wei,&nbsp;Kai Wu,&nbsp;HuaBin Zhao,&nbsp;Guan Yang,&nbsp;Jiangchao Zhao,&nbsp;Ying Li,&nbsp;Chengdong Wang","doi":"10.1002/imt2.171","DOIUrl":"10.1002/imt2.171","url":null,"abstract":"<p>In this study, we have successfully constructed a comprehensive database of metagenome-assembled genomes (MAGs) pertaining to the gut microbiota of the giant panda. Through our analysis, we have identified significant reservoirs of antibiotic resistance genes (ARGs), namely <i>Escherichia coli, Citrobacter portucalensis</i>, and <i>Klebsiella pneumoniae</i>. Furthermore, we have elucidated the primary contributors to ARGs, including <i>Streptococcus alactolyticus</i> and <i>Clostridium SGBP116</i>, in both captive and wild pandas. Additionally, our findings have demonstrated a higher prevalence of ARGs in the metagenome, with notable expression of the <i>RPOB2</i> gene in <i>S. alactolyticus</i>. Crucially, 1217 ARGs shared homology with human gut ARGs, underscoring the interaction relationship between pandas and human microbiomes. These findings are instrumental in understanding the antibiotic resistance landscape in the giant panda's gut, providing a framework for developing strategies to combat antibiotic resistance and safeguard the health of this endangered species.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.171","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139800015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life","authors":"Xinming Xu,&nbsp;Qingying Feng,&nbsp;Tao Zhang,&nbsp;Yunlong Gao,&nbsp;Qu Cheng,&nbsp;Wanqiu Zhang,&nbsp;Qinglong Wu,&nbsp;Ke Xu,&nbsp;Yucan Li,&nbsp;Nhu Nguyen,&nbsp;Diana H. Taft,&nbsp;David A. Mills,&nbsp;Danielle G. Lemay,&nbsp;Weiyun Zhu,&nbsp;Shengyong Mao,&nbsp;Anyun Zhang,&nbsp;Kelin Xu,&nbsp;Jinxin Liu","doi":"10.1002/imt2.169","DOIUrl":"10.1002/imt2.169","url":null,"abstract":"<p>The infant gut microbiome is increasingly recognized as a reservoir of antibiotic resistance genes, yet the assembly of gut resistome in infants and its influencing factors remain largely unknown. We characterized resistome in 4132 metagenomes from 963 infants in six countries and 4285 resistance genes were observed. The inherent resistome pattern of healthy infants (<i>N</i> = 272) could be distinguished by two stages: a multicompound resistance phase (Months 0–7) and a tetracycline-mupirocin-β-lactam-dominant phase (Months 8–14). Microbial taxonomy explained 40.7% of the gut resistome of healthy infants, with <i>Escherichia</i> (25.5%) harboring the most resistance genes. In a further analysis with all available infants (<i>N</i> = 963), we found age was the strongest influencer on the resistome and was negatively correlated with the overall resistance during the first 3 years (<i>p</i> &lt; 0.001). Using a random-forest approach, a set of 34 resistance genes could be used to predict age (<i>R</i>² = 68.0%). Leveraging microbial host inference analyses, we inferred the age-dependent assembly of infant resistome was a result of shifts in the gut microbiome, primarily driven by changes in taxa that disproportionately harbor resistance genes across taxa (e.g., <i>Escherichia coli</i> more frequently harbored resistance genes than other taxa). We performed metagenomic functional profiling and metagenomic assembled genome analyses whose results indicate that the development of gut resistome was driven by changes in microbial carbohydrate metabolism, with an increasing need for carbohydrate-active enzymes from <i>Bacteroidota</i> and a decreasing need for <i>Pseudomonadota</i> during infancy. Importantly, we observed increased acquired resistance genes over time, which was related to increased horizontal gene transfer in the developing infant gut microbiome. In summary, infant age was negatively correlated with antimicrobial resistance gene levels, reflecting a composition shift in the gut microbiome, likely driven by the changing need for microbial carbohydrate metabolism during early life.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.169","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140473826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"“Nutrient–fungi–host” tripartite interaction in cancer progression","authors":"Di Wu,&nbsp;Yun-Xuan Guan,&nbsp;Chen-Hao Li,&nbsp;Quan Zheng,&nbsp;Zuo-Jing Yin,&nbsp;Hui Wang,&nbsp;Ning-Ning Liu","doi":"10.1002/imt2.170","DOIUrl":"10.1002/imt2.170","url":null,"abstract":"<p>The human microbiome exhibits a profound connection with the cancer development, progression, and therapeutic response, with particular emphasis on its components of the mycobiome, which are still in the early stages of research. In this review, we comprehensively summarize cancer-related symbiotic and pathogenic fungal genera. The intricate mechanisms through which fungi impact cancer as an integral member of both gut and tissue-resident microbiomes are further discussed. In addition, we shed light on the pivotal physiological roles of various nutrients, including cholesterol, carbohydrates, proteins and minerals, in facilitating the growth, reproduction, and invasive pathogenesis of the fungi. While our exploration of the interplay between nutrients and cancer, mediated by the mycobiome, is ongoing, the current findings have yet to yield conclusive results. Thus, delving into the relationship between nutrients and fungal pathogenesis in cancer development and progression would provide valuable insights into anticancer therapy and foster precision nutrition and individualized treatments that target fungi from bench to bedside.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.170","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139595164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Changes in seminal plasma microecological dynamics and the mechanistic impact of core metabolite hexadecanamide in asthenozoospermia patients","authors":"Baoquan Han,&nbsp;Yongyong Wang,&nbsp;Wei Ge,&nbsp;Junjie Wang,&nbsp;Shuai Yu,&nbsp;Jiamao Yan,&nbsp;Lei Hua,&nbsp;Xiaoyuan Zhang,&nbsp;Zihui Yan,&nbsp;Lu Wang,&nbsp;Jinxin Zhao,&nbsp;Cong Huang,&nbsp;Bo Yang,&nbsp;Yan Wang,&nbsp;Qian Ma,&nbsp;Yong Zhao,&nbsp;Hui Jiang,&nbsp;Yunqi Zhang,&nbsp;Shaolin Liang,&nbsp;Jianjuan Zhao,&nbsp;Zhongyi Sun,&nbsp;Wei Shen,&nbsp;Yaoting Gui","doi":"10.1002/imt2.166","DOIUrl":"10.1002/imt2.166","url":null,"abstract":"<p>Asthenozoospermia (AZS) is a prevalent contributor to male infertility, characterized by a substantial decline in sperm motility. In recent years, large-scale studies have explored the interplay between the male reproductive system's microecology and its implications for reproductive health. Nevertheless, the direct association between seminal microecology and male infertility pathogenesis remains inconclusive. This study used 16S rDNA sequencing and multi-omics analysis to conduct a comprehensive investigation of the seminal microbial community and metabolites in AZS patients. Patients were categorized into four distinct groups: Normal, mild AZS (AZS-I), moderate AZS (AZS-II), and severe AZS (AZS-III). Microbiome differential abundance analysis revealed significant differences in microbial composition and metabolite profiles within the seminal plasma of these groups. Subsequently, patients were classified into a control group (Normal and AZS-I) and an AZS group (AZS-II and AZS-III). Correlation and cross-reference analyses identified distinct microbial genera and metabolites. Notably, the AZS group exhibited a reduced abundance of bacterial genera such as <i>Pseudomonas, Serratia</i>, and <i>Methylobacterium-Methylorubrum</i> in seminal plasma, positively correlating with core differential metabolite (hexadecanamide). Conversely, the AZS group displayed an increased abundance of bacterial genera such as <i>Uruburuella, Vibrio</i>, and <i>Pseudoalteromonas</i>, with a negative correlation with core differential metabolite (hexadecanamide). In vitro and in vivo experiments validated that hexadecanamide significantly enhanced sperm motility. Using predictive metabolite-targeting gene analysis and single-cell transcriptome sequencing, we profiled the gene expression of candidate target genes <i>PAOX</i> and <i>CA2</i>. Protein immunoblotting techniques validated the upregulation protein levels of PAOX and CA2 in sperm samples after hexadecanamide treatment, enhancing sperm motility. In conclusion, this study uncovered a significant correlation between six microbial genera in seminal plasma and the content of the metabolite hexadecanamide, which is related to AZS. Hexadecanamide notably enhances sperm motility, suggesting its potential integration into clinical strategies for managing AZS, providing a foundational framework for diagnostic and therapeutic advancements.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.166","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139595847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Intestinal flora and pregnancy complications: Current insights and future prospects","authors":"Zhenyu Tian,&nbsp;Xinjie Zhang,&nbsp;Guixiang Yao,&nbsp;Jiajia Jin,&nbsp;Tongxue Zhang,&nbsp;Chunhua Sun,&nbsp;Zhe Wang,&nbsp;Qunye Zhang","doi":"10.1002/imt2.167","DOIUrl":"10.1002/imt2.167","url":null,"abstract":"<p>Numerous studies have demonstrated the pivotal roles of intestinal microbiota in many physiopathological processes through complex interactions with the host. As a unique period in a woman's lifespan, pregnancy is characterized by changes in hormones, immunity, and metabolism. The gut microbiota also changes during this period and plays a crucial role in maintaining a healthy pregnancy. Consequently, anomalies in the composition and function of the gut microbiota, namely, gut microbiota dysbiosis, can predispose individuals to various pregnancy complications, posing substantial risks to both maternal and neonatal health. However, there are still many controversies in this field, such as “sterile womb” versus “in utero colonization.” Therefore, a thorough understanding of the roles and mechanisms of gut microbiota in pregnancy and its complications is essential to safeguard the health of both mother and child. This review provides a comprehensive overview of the changes in gut microbiota during pregnancy, its abnormalities in common pregnancy complications, and potential etiological implications. It also explores the potential of gut microbiota in diagnosing and treating pregnancy complications and examines the possibility of gut-derived bacteria residing in the uterus/placenta. Our aim is to expand knowledge in maternal and infant health from the gut microbiota perspective, aiding in developing new preventive and therapeutic strategies for pregnancy complications based on intestinal microecology.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.167","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139608189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Storage-D: A user-friendly platform that enables practical and personalized DNA data storage","authors":"Xiaoluo Huang,&nbsp;Junting Cui,&nbsp;Wei Qiang,&nbsp;Jianwen Ye,&nbsp;Yu Wang,&nbsp;Xinying Xie,&nbsp;Yuanzhen Li,&nbsp;Junbiao Dai","doi":"10.1002/imt2.168","DOIUrl":"10.1002/imt2.168","url":null,"abstract":"<p>Deoxyribonucleic acid (DNA) has been suggested as a very promising medium for data storage in recent years. Although numerous studies have advocated for DNA data storage, its practical application remains obscure and there is a lack of a user-oriented platform. Here, we developed a DNA data storage platform, named Storage-D, which allows users to convert their data into DNA sequences of any length and vice versa by selecting algorithms, error-correction, random-access, and codec pin strategies in terms of their own choice. It incorporates a newly designed “Wukong” algorithm, which provides over 20 trillion codec pins for data privacy use. This algorithm can also control GC content to the selected standard, as well as adjust the homopolymer run length to a defined level, while maintaining a high coding potential of ~1.98 bis/nt, allowing it to outperform previous algorithms. By connecting to a commercial DNA synthesis and sequencing platform with “Storage-D,” we successfully stored “Diagnosis and treatment protocol for COVID-19 patients” into 200 nt oligo pools in vitro, and 500 bp genes in vivo which replicated in both normal and extreme bacteria. Together, this platform allows for practical and personalized DNA data storage, potentially with a wide range of applications.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.168","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139609967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}